The Genomics Research and Innovation Network: creating an interoperable, federated, genomics learning system
The Genomics Research and Innovation Network: creating an interoperable, federated, genomics learning system
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DOI：
10.1038/s41436-019-0646-3
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发表时间：
2020-02-01
影响因子：
8.8
通讯作者：
Zhang, Yu
中科院分区：
文献类型：
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作者：
Mandl, Kenneth D.;Glauser, Tracy;Zhang, Yu
目的临床医生和研究人员必须将患者的遗传变异与基于人群的参考资料结合起来，并进行详细的表型分析。我们寻求建立全球可扩展的技术、政策和程序，以便在各护理中心共享广泛同意的队列的生物样本和相关基因组和表型数据。方法三家全国领先的儿童医院启动了基因组研究和创新网络（GRIN），联合信息技术基础设施，协调生物库协议和材料转移协议。完成了癫痫和身材矮小的试点研究，以设计和测试合作模式。结果协调一致的、广泛同意的机构审查委员会（IRB）方案获得批准，并用于生物库招募，创建不断扩大的、兼容的生物库。在三家医院的基因型-表型数据库上建立了开源联合查询基础设施。研究者安全地访问GRIN平台，以准备研究查询，接收每个生物库中具有特定表型或基因型的患者的汇总计数。经过适当的批准，去识别数据将导出到共享的分析工作区。所有研究中心的研究人员都积极合作开展了试点研究，并发表了多篇论文。调查人员也开始成功地利用基础设施申请赠款。GRIN合作为可扩展的基因组研究网络建立了技术，政策和程序。
Purpose Clinicians and researchers must contextualize a patient's genetic variants against population-based references with detailed phenotyping. We sought to establish globally scalable technology, policy, and procedures for sharing biosamples and associated genomic and phenotypic data on broadly consented cohorts, across sites of care. Methods Three of the nation's leading children's hospitals launched the Genomic Research and Innovation Network (GRIN), with federated information technology infrastructure, harmonized biobanking protocols, and material transfer agreements. Pilot studies in epilepsy and short stature were completed to design and test the collaboration model. Results Harmonized, broadly consented institutional review board (IRB) protocols were approved and used for biobank enrollment, creating ever-expanding, compatible biobanks. An open source federated query infrastructure was established over genotype-phenotype databases at the three hospitals. Investigators securely access the GRIN platform for prep to research queries, receiving aggregate counts of patients with particular phenotypes or genotypes in each biobank. With proper approvals, de-identified data is exported to a shared analytic workspace. Investigators at all sites enthusiastically collaborated on the pilot studies, resulting in multiple publications. Investigators have also begun to successfully utilize the infrastructure for grant applications. Conclusions The GRIN collaboration establishes the technology, policy, and procedures for a scalable genomic research network.